##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD INSTALL DeMixT
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.23-bioc/R/site-library’
* installing *source* package ‘DeMixT’ ...
** this is package ‘DeMixT’ version ‘1.99.0’
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0’
using C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0’
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I/usr/local/include   -fopenmp -I/home/biocbuild/bbs-3.23-bioc/R/include -fpic  -g -O2  -Wall -Werror=format-security -c DeMixNB.c -o DeMixNB.o
In file included from DeMixNB.c:6:
DeMixNB.h:4:15: warning: ‘stirling_approx’ defined but not used [-Wunused-function]
    4 | static double stirling_approx(double z)
      |               ^~~~~~~~~~~~~~~
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I/usr/local/include   -fopenmp -I/home/biocbuild/bbs-3.23-bioc/R/include -fpic  -g -O2  -Wall -Werror=format-security -c DeMixT.c -o DeMixT.o
DeMixT.c: In function ‘Tdemix’:
DeMixT.c:37:45: warning: variable ‘st2_sig_2’ set but not used [-Wunused-but-set-variable]
   37 |   double *st1_mu_2, *st2_mu_2, *st1_sig_2, *st2_sig_2;
      |                                             ^~~~~~~~~
DeMixT.c:37:33: warning: variable ‘st1_sig_2’ set but not used [-Wunused-but-set-variable]
   37 |   double *st1_mu_2, *st2_mu_2, *st1_sig_2, *st2_sig_2;
      |                                 ^~~~~~~~~
DeMixT.c:37:22: warning: variable ‘st2_mu_2’ set but not used [-Wunused-but-set-variable]
   37 |   double *st1_mu_2, *st2_mu_2, *st1_sig_2, *st2_sig_2;
      |                      ^~~~~~~~
DeMixT.c:37:11: warning: variable ‘st1_mu_2’ set but not used [-Wunused-but-set-variable]
   37 |   double *st1_mu_2, *st2_mu_2, *st1_sig_2, *st2_sig_2;
      |           ^~~~~~~~
DeMixT.c: In function ‘gettumor’:
DeMixT.c:592:21: warning: variable ‘obj_new’ set but not used [-Wunused-but-set-variable]
  592 |     double obj_old, obj_new;
      |                     ^~~~~~~
DeMixT.c:592:12: warning: variable ‘obj_old’ set but not used [-Wunused-but-set-variable]
  592 |     double obj_old, obj_new;
      |            ^~~~~~~
DeMixT.c: In function ‘getpi’:
DeMixT.c:1281:21: warning: variable ‘obj_new’ set but not used [-Wunused-but-set-variable]
 1281 |     double obj_old, obj_new;
      |                     ^~~~~~~
DeMixT.c:1281:12: warning: variable ‘obj_old’ set but not used [-Wunused-but-set-variable]
 1281 |     double obj_old, obj_new;
      |            ^~~~~~~
DeMixT.c: In function ‘getspikeinpi’:
DeMixT.c:1308:25: warning: variable ‘obj_new’ set but not used [-Wunused-but-set-variable]
 1308 |         double obj_old, obj_new;
      |                         ^~~~~~~
DeMixT.c:1308:16: warning: variable ‘obj_old’ set but not used [-Wunused-but-set-variable]
 1308 |         double obj_old, obj_new;
      |                ^~~~~~~
DeMixT.c: In function ‘getpiT’:
DeMixT.c:1323:21: warning: variable ‘obj_new’ set but not used [-Wunused-but-set-variable]
 1323 |     double obj_old, obj_new;
      |                     ^~~~~~~
DeMixT.c:1323:12: warning: variable ‘obj_old’ set but not used [-Wunused-but-set-variable]
 1323 |     double obj_old, obj_new;
      |            ^~~~~~~
DeMixT.c: In function ‘Tdemix’:
DeMixT.c:196:11: warning: ‘Tavgtmp’ may be used uninitialized [-Wmaybe-uninitialized]
  196 |         if(Tavgtmp <= 0) Tavgtmp = exp(10*log(2.0) + p->Tsigma[j]/2.0*pow(log(2.0), 2.0));
      |           ^
DeMixT.c:178:12: note: ‘Tavgtmp’ was declared here
  178 |     double Tavgtmp;
      |            ^~~~~~~
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I/usr/local/include   -fopenmp -I/home/biocbuild/bbs-3.23-bioc/R/include -fpic  -g -O2  -Wall -Werror=format-security -c init.c -o init.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I/usr/local/include   -fopenmp -I/home/biocbuild/bbs-3.23-bioc/R/include -fpic  -g -O2  -Wall -Werror=format-security -c registerDynamicSymbol.c -o registerDynamicSymbol.o
g++ -std=gnu++20 -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I/usr/local/include   -fopenmp -I/home/biocbuild/bbs-3.23-bioc/R/include -fpic  -g -O2  -Wall -Werror=format-security  -c Profile_2D.cpp -o Profile_2D.o
g++ -std=gnu++20 -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I/usr/local/include   -fopenmp -I/home/biocbuild/bbs-3.23-bioc/R/include -fpic  -g -O2  -Wall -Werror=format-security  -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++20 -shared -L/usr/local/lib -o DeMixT.so DeMixNB.o DeMixT.o init.o registerDynamicSymbol.o Profile_2D.o RcppExports.o -fopenmp -llapack -L/home/biocbuild/bbs-3.23-bioc/R/lib -lRblas -lgfortran -lm -lquadmath
installing to /home/biocbuild/bbs-3.23-bioc/R/site-library/00LOCK-DeMixT/00new/DeMixT/libs
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (DeMixT)